MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·Or in RNA crystal structures in the full dataset (switch to benchmark dataset) Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "PDB ID" or "Mg2+ ID" Page 8 of 48 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4eja A7073 Oph·Or 2   0.04   0.32   0.76 no 4kfh A1902 Oph·Or 2   0.04   0.21   0.58 no 4ji7 A1651 Oph·Or 2   0.04   0.56   0.83 no 1vx9 A3183 Oph·Or 2   0.04   0.32   0.09 no 4l6j A4693 Oph·Or 2   0.04   0.29   0.44 no 4qct A3017 Oph·Or 2   0.04   0.31   0.66 no 4ej9 A7101 Oph·Or 2   0.04   0.17   0.22 no 4qcr A3207 Oph·Or 2   0.04   0.53   0.70 no 4l6j A6000 Oph·Or 2   0.04   0.58   0.52 no 4nw1 A3129 Oph·Or 2   0.04   0.65   0.85 no 2x9t Z508 Oph·Or 2   0.04   0.51   0.91 no 4ji0 A1790 Oph·Or 2   0.04   0.28   0.53 no 4dv3 A1805 Oph·Or 2   0.04   0.55   0.68 no 3sgf A3231 Oph·Or 2   0.04   0.37   0.71 no 2uuc Z1185 Oph·Or 2   0.04   0.47   0.97 no 4qcz E3001 Oph·Or 2   0.04   0.34   0.60 no 4ji2 A1791 Oph·Or 2   0.04   0.53   0.87 no 4dv7 A1726 Oph·Or 2   0.04   0.54   0.94 no 4dr1 A1762 Oph·Or 2   0.04   0.58   0.88 no 4l6j A4253 Oph·Or 2   0.04   0.26   0.92 no 3u5d 14329 Oph·Or 2   0.04   0.70   0.68 no 4b3r A2552 Oph·Or 2   0.04   0.53   0.84 no 3pyr A3098 Oph·Or 2   0.04   0.28   0.49 no 2wh1 Z510 Oph·Or 2   0.04   0.35   0.59 no 4byc A3902 Oph·Or 2   0.04   0.64   0.87 no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>